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/* *
* This file is part of the ESO X-shooter Pipeline *
* Copyright (C) 2006 European Southern Observatory *
* *
* This library is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the Free Software *
* Foundation, 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA *
* */
/*
* $Author: amodigli $
* $Date: 2013-03-18 11:40:35 $
* $Revision: 1.98 $
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
/*----------------------------------------------------------------------------*/
/**
* @defgroup xsh_orderpos xsh_orderpos
* @ingroup recipes
*
* This recipe calculates the position of the orders from a flat illumination
* See man-page for details.
*/
/*----------------------------------------------------------------------------*/
/**@{*/
/*-----------------------------------------------------------------------------
Includes
----------------------------------------------------------------------------*/
/* DRL steps */
/* Error handling */
#include <xsh_error.h>
/* Utility fonctions */
#include <xsh_pfits_qc.h>
#include <xsh_utils.h>
#include <xsh_msg.h>
/* DFS functions */
#include <xsh_dfs.h>
/* DRL functions */
#include <xsh_drl.h>
#include <xsh_drl_check.h>
#include <xsh_data_instrument.h>
#include <xsh_model_arm_constants.h>
/* Library */
#include <cpl.h>
/*-----------------------------------------------------------------------------
Defines
----------------------------------------------------------------------------*/
#define RECIPE_ID "xsh_orderpos"
#define RECIPE_AUTHOR "L.Guglielmi,R.Haigron,P.Goldoni,F.Royer, A. Modigliani"
#define RECIPE_CONTACT "amodigli@eso.org"
/*-----------------------------------------------------------------------------
Functions prototypes
----------------------------------------------------------------------------*/
/*
* Plugin initalization, execute and cleanup handlers
*/
static int xsh_orderpos_create(cpl_plugin *);
static int xsh_orderpos_exec(cpl_plugin *);
static int xsh_orderpos_destroy(cpl_plugin *);
/* The actual executor function */
static void xsh_orderpos(cpl_parameterlist *, cpl_frameset *);
/*-----------------------------------------------------------------------------
Static variables
----------------------------------------------------------------------------*/
static char xsh_orderpos_description_short[] =
"Create the orders centre traces table file";
static char xsh_orderpos_description[] =
"This recipe creates the orders centre traces table.\n\
Input Frames for UVB and VIS:\n\
Raw file (Tag = ORDERDEF_arm_D2)\n\
Master Dark (Tag = MASTER_DARK_arm)\n\
Master Bias (Tag = MASTER_BIAS_arm)\n\
Input Frames for NIR:\n\
Raw file ON(Tag = ORDERDEF_NIR_ON)\n\
Raw file OFF(Tag = ORDERDEF_NIR_OFF)\n\
Input Frames for all arms\n\
Guess order table (Tag = ORDER_TAB_GUESS_arm)\n\
Spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)\n\
- [OPTIONAL] A map of non linear bad pixels (Format=QUP, Tag = BP_MAP_NL_arm)\n\
- [OPTIONAL] A map of reference bad pixels (Format = QUP,RAW, Tag = BP_MAP_RP_arm)\n\
Prepare PRE structures.\n\
For NIR, subtract NIR-OFF from NIR-ON.\n\
For UVB and NIR, Substract the master Bias and master dark.\n\
Detect Orders and calculate the order table.\n\
The final products are:\n\
An updated Order Table, PRO.CATG=ORDER_TABLE_CENTR_arm.\n\
A order trace residuals Table, PRO.CATG=ORDERPOS_RESID_TAB_arm.\n\
The order pos frame bias subtracted, PRO.CATG=ORDERDEF_ON_arm.\n";
/*-----------------------------------------------------------------------------
Functions code
----------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------*/
/**
@brief Build the list of available plugins, for this module.
@param list the plugin list
@return 0 if everything is ok, -1 otherwise
Create the recipe instance and make it available to the application using the
interface. This function is exported.
*/
/*----------------------------------------------------------------------------*/
int cpl_plugin_get_info(cpl_pluginlist *list) {
cpl_recipe *recipe = NULL;
cpl_plugin *plugin = NULL;
recipe = cpl_calloc(1, sizeof(*recipe));
if ( recipe == NULL ){
return -1;
}
plugin = &recipe->interface ;
cpl_plugin_init(plugin,
CPL_PLUGIN_API, /* Plugin API */
XSH_BINARY_VERSION, /* Plugin version */
CPL_PLUGIN_TYPE_RECIPE, /* Plugin type */
RECIPE_ID, /* Plugin name */
xsh_orderpos_description_short, /* Short help */
xsh_orderpos_description, /* Detailed help */
RECIPE_AUTHOR, /* Author name */
RECIPE_CONTACT, /* Contact address */
xsh_get_license(), /* Copyright */
xsh_orderpos_create,
xsh_orderpos_exec,
xsh_orderpos_destroy);
cpl_pluginlist_append(list, plugin);
return (cpl_error_get_code() != CPL_ERROR_NONE);
}
/*----------------------------------------------------------------------------*/
/**
@brief Setup the recipe options
@param plugin the plugin
@return 0 if everything is ok
Create the recipe instance and make it available to the application using the
interface.
*/
/*----------------------------------------------------------------------------*/
static int xsh_orderpos_create(cpl_plugin *plugin){
cpl_recipe *recipe = NULL;
xsh_detect_continuum_param param = { 5, 0, 5,
DETECT_CONTINUUM_POLYNOMIAL_DEGREE,
1, 0.,
/* fmtchk*/ 20, 50, 140., 2., 0 } ;
/* Reset library state */
xsh_init();
/* Check input */
assure( plugin != NULL, CPL_ERROR_NULL_INPUT, "Null plugin");
/* Get the recipe out of the plugin */
assure( cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE,
CPL_ERROR_TYPE_MISMATCH,
"Plugin is not a recipe");
recipe = (cpl_recipe *)plugin;
/* Create the parameter list in the cpl_recipe object */
recipe->parameters = cpl_parameterlist_new();
assure( recipe->parameters != NULL,
CPL_ERROR_ILLEGAL_OUTPUT,
"Memory allocation failed!");
/* Set generic parameters (common to all recipes) */
check( xsh_parameters_generic( RECIPE_ID, recipe->parameters ) ) ;
xsh_parameters_decode_bp(RECIPE_ID,recipe->parameters,-1);
check( xsh_parameters_pre_overscan( RECIPE_ID, recipe->parameters ) ) ;
check(xsh_parameters_detect_continuum_create(RECIPE_ID,
recipe->parameters,
param));
check( xsh_parameters_clipping_dcn_create( RECIPE_ID,
recipe->parameters ) ) ;
cleanup:
if ( cpl_error_get_code() != CPL_ERROR_NONE ){
xsh_error_dump(CPL_MSG_ERROR);
return 1;
}
else {
return 0;
}
}
/*----------------------------------------------------------------------------*/
/**
@brief Execute the plugin instance given by the interface
@param plugin the plugin
@return 0 if everything is ok
*/
/*----------------------------------------------------------------------------*/
static int xsh_orderpos_exec(cpl_plugin *plugin) {
cpl_recipe *recipe = NULL;
/* Check parameter */
assure( plugin != NULL, CPL_ERROR_NULL_INPUT, "Null plugin" );
/* Get the recipe out of the plugin */
assure( cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE,
CPL_ERROR_TYPE_MISMATCH, "Plugin is not a recipe");
recipe = (cpl_recipe *)plugin;
/* Check recipe */
xsh_orderpos(recipe->parameters, recipe->frames);
cleanup:
if ( cpl_error_get_code() != CPL_ERROR_NONE ) {
xsh_error_dump(CPL_MSG_ERROR);
/* RESTORE the error context */
cpl_error_reset();
return 1;
}
else {
return 0;
}
}
/*----------------------------------------------------------------------------*/
/**
@brief Destroy what has been created by the 'create' function
@param plugin the plugin
@return 0 if everything is ok
*/
/*----------------------------------------------------------------------------*/
static int xsh_orderpos_destroy(cpl_plugin *plugin)
{
cpl_recipe *recipe = NULL;
/* Check parameter */
assure( plugin != NULL, CPL_ERROR_NULL_INPUT, "Null plugin" );
/* Get the recipe out of the plugin */
assure( cpl_plugin_get_type(plugin) == CPL_PLUGIN_TYPE_RECIPE,
CPL_ERROR_TYPE_MISMATCH, "Plugin is not a recipe");
recipe = (cpl_recipe *)plugin;
xsh_free_parameterlist(&recipe->parameters);
cleanup:
if (cpl_error_get_code() != CPL_ERROR_NONE)
{
return 1;
}
else
{
return 0;
}
}
/*----------------------------------------------------------------------------*/
/**
@brief Interpret the command line options and execute the data processing
@param parameters the parameters list
@param frameset the frames list
In case of failure the cpl_error_code is set.
*/
/*----------------------------------------------------------------------------*/
static void xsh_orderpos(cpl_parameterlist* parameters,
cpl_frameset* frameset)
{
const char* recipe_tags[1] = {XSH_ORDERDEF};
int recipe_tags_size = 1;
/* Intermediate frames */
cpl_frameset* raws = NULL;
cpl_frameset* calib = NULL;
cpl_frame* bpmap = NULL;
cpl_frame* master_bias = NULL;
cpl_frame* master_dark = NULL;
cpl_frame * order_tab_guess = NULL ;
cpl_frame * orderframe = NULL ;
cpl_frame * spectralformat_frame = NULL ;
cpl_frame * rmbias = NULL ;
cpl_frame * intFrame = NULL ; /**< The frame where to find orders */
cpl_frame * nir_on = NULL ; /**< Do NOT deallocated this pointer ! */
cpl_frame * nir_off = NULL ; /**< Do NOT deallocated this pointer ! */
/* Product frames */
cpl_frame * resFrame = NULL ;
/* Other */
xsh_detect_continuum_param * detect_param = NULL ;
xsh_instrument* instrument = NULL;
xsh_clipping_param * dcn_clipping_param = NULL;
cpl_frame* resid_tab=NULL;
char tag[128];
char fname[128] ;
int pre_overscan_corr=0;
/**************************************************************************/
/* DFS management */
/**************************************************************************/
check( xsh_begin( frameset, parameters, &instrument, &raws, &calib,
recipe_tags, recipe_tags_size,
RECIPE_ID, XSH_BINARY_VERSION,
xsh_orderpos_description_short ) ) ;
/* Why */
check( xsh_instrument_update_lamp( instrument, XSH_LAMP_UNDEFINED));
xsh_recipe_params_check(parameters,instrument,RECIPE_ID);
/**************************************************************************/
/* Recipe frames */
/**************************************************************************/
check( spectralformat_frame = xsh_find_frame_with_tag( calib,
XSH_SPECTRAL_FORMAT, instrument));
check(bpmap=xsh_check_load_master_bpmap(calib,instrument,RECIPE_ID));
if ( xsh_instrument_get_arm(instrument) == XSH_ARM_NIR ) {
check( nir_on = xsh_find_raw_orderdef_nir ( raws ) ) ;
check( nir_off = xsh_find_raw_orderdef_nir_off ( raws ) ) ;
}
else {
check( orderframe = xsh_find_raw_orderdef_vis_uvb( raws ) ) ;
if((master_bias = xsh_find_frame_with_tag(calib,XSH_MASTER_BIAS,
instrument)) == NULL) {
xsh_msg_warning("Frame %s not provided",XSH_MASTER_BIAS);
xsh_error_reset();
}
if((master_dark = xsh_find_frame_with_tag(calib,XSH_MASTER_DARK,
instrument)) == NULL){
xsh_msg_warning("Frame %s not provided",XSH_MASTER_DARK);
xsh_error_reset();
}
}
if(NULL== (order_tab_guess = xsh_find_frame_with_tag(calib,
XSH_ORDER_TAB_GUESS,
instrument)) ) {
xsh_msg_error("you must provide an input %s_%s table",XSH_ORDER_TAB_GUESS,
xsh_instrument_arm_tostring(instrument));
goto cleanup;
}
check( xsh_instrument_update_from_spectralformat( instrument,
spectralformat_frame));
/**************************************************************************/
/* Recipe parameters */
/**************************************************************************/
check( pre_overscan_corr = xsh_parameters_get_int( parameters, RECIPE_ID,
"pre-overscan-corr"));
check(detect_param=xsh_parameters_detect_continuum_get( RECIPE_ID,
parameters)) ;
xsh_msg_dbg_low("Search Window: %d, Running Window: %d, Fit Window: %d",
detect_param->search_window, detect_param->running_window,
detect_param->fit_window ) ;
xsh_msg_dbg_low( "Polynomial degree: %d, Step: %d", detect_param->poly_degree,
detect_param->poly_step ) ;
check( dcn_clipping_param = xsh_parameters_clipping_dcn_get( RECIPE_ID,
parameters ));
/* not needed as Daniel says current defaults are robust for any arm
check(xsh_params_set_defaults(parameters,instrument,detect_param,
dcn_clipping_param));
*/
/**************************************************************************/
/* Recipe code */
/**************************************************************************/
xsh_msg( "Working on Arm %s", xsh_instrument_arm_tostring(instrument ) ) ;
check(xsh_prepare(raws, bpmap, master_bias, XSH_ORDERDEF, instrument,pre_overscan_corr,CPL_TRUE));
/*
from raws frameset one should use only the single (or the 2 in case of
NIR) flat frames "ORDERDEF_arm_D2"
*/
if ( xsh_instrument_get_arm(instrument) == XSH_ARM_NIR ) {
/* subtract Off frame */
check(intFrame=xsh_pre_frame_subtract( nir_on, nir_off,
"ON-OFF_NIR.fits",instrument,1 ) ) ;
}
else {
/* UVB and VIS */
if(master_bias!= NULL) {
/* correct bias level */
xsh_msg( "Substract bias" ) ;
check(rmbias = xsh_subtract_bias( orderframe, master_bias, instrument,"ORDERDEF_",pre_overscan_corr,0));
} else {
rmbias=cpl_frame_duplicate(orderframe);
}
/* correct dark level */
if(master_dark!= NULL) {
xsh_msg( "Substract dark" ) ;
sprintf( fname, "ORDERPOS_%s_DARK.fits",
xsh_instrument_arm_tostring(instrument ) ) ;
check(intFrame = xsh_subtract_dark(rmbias, master_dark,
fname, instrument));
} else {
intFrame=cpl_frame_duplicate(rmbias);
}
}
/* check on binning: operations takes orderdef frames also in bin mode but the pipeline supports only
* unbinned orderdef frame input */
if ( xsh_instrument_get_arm(instrument) != XSH_ARM_NIR){
check(xsh_check_input_is_unbinned(intFrame));
}
/*
TODO:
Add an option "--recover" using a function "xsh_find_order" instead
of detect_continuum to create an order table.
xsh_find_order does NOT use any order table, but seraches for
maximum along Y for x = nx/2, x = nx/2 - step, ... x = nx/2 + step ...
*/
/* Detect Continuum */
xsh_msg("Calling detect continuum" ) ;
/* the following generate a leak */
check_msg( resFrame = xsh_detect_continuum( intFrame, order_tab_guess,
spectralformat_frame,
detect_param,
dcn_clipping_param,
instrument, &resid_tab ),
"Error in xsh_detect_continuum, try to increase detectcontinuum-fit-win-hsize or detectcontinuum-ordertab-deg-y or detectcontinuum-clip-sigma or detectcontinuum-search-win-hsize" ) ;
/* monitor input frame flux */
check(xsh_monitor_flux( intFrame, resFrame, instrument, XSH_QC_FLUX));
/**************************************************************************/
/* Products */
/**************************************************************************/
xsh_msg( "Save Order Table product" ) ;
check(xsh_add_product_table( resFrame, frameset, parameters, RECIPE_ID,
instrument,NULL));
check(xsh_add_product_table(resid_tab, frameset, parameters, RECIPE_ID,
instrument,NULL));
if ( xsh_instrument_get_arm(instrument) == XSH_ARM_NIR ) {
sprintf(tag,"ORDERDEF_ON");
check(xsh_add_product_image(intFrame,frameset,parameters,RECIPE_ID,instrument,tag));
} else {
sprintf(tag,"ORDERDEF_ON");
check(xsh_add_product_image(rmbias,frameset,parameters,RECIPE_ID,instrument,tag));
}
cleanup:
xsh_end( RECIPE_ID, frameset, parameters );
XSH_FREE( dcn_clipping_param );
XSH_FREE( detect_param );
xsh_instrument_free(&instrument );
xsh_free_frameset(&raws);
xsh_free_frameset(&calib);
xsh_free_frame( &resFrame) ;
xsh_free_frame( &resid_tab) ;
xsh_free_frame(&rmbias);
xsh_free_frame(&bpmap);
xsh_free_frame(&intFrame);
return;
}
/**@}*/
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